phylogenetic network

{{short description|Graph used to visualize evolutionary relationships, including reticulation events}}

A phylogenetic network is any graph used to visualize evolutionary relationships (either abstractly or explicitly){{cite journal | vauthors = Huson DH, Scornavacca C | title = A survey of combinatorial methods for phylogenetic networks | journal = Genome Biology and Evolution | volume = 3 | pages = 23–35 | date = 2011 | pmid = 21081312 | pmc = 3017387 | doi = 10.1093/gbe/evq077 }} between nucleotide sequences, genes, chromosomes, genomes, or species.{{cite book | vauthors = Huson DH, Rupp R, Scornavacca C | url = http://www.phylogenetic-networks.org/ | title = Phylogenetic Networks | location = Cambridge University Press | date = 2010 | access-date = 2010-03-23 | archive-url = https://web.archive.org/web/20140714175751/http://www.phylogenetic-networks.org/ | archive-date = 2014-07-14 | url-status = dead }} They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (a hierarchy of nodes, each with only one parent).{{cite journal | vauthors = Arenas M, Valiente G, Posada D | title = Characterization of reticulate networks based on the coalescent with recombination | journal = Molecular Biology and Evolution | volume = 25 | issue = 12 | pages = 2517–20 | date = December 2008 | pmid = 18927089 | pmc = 2582979 | doi = 10.1093/molbev/msn219 }} Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree,{{cite journal | vauthors = Huson DH, Bryant D | title = Application of phylogenetic networks in evolutionary studies | journal = Molecular Biology and Evolution | volume = 23 | issue = 2 | pages = 254–67 | date = February 2006 | pmid = 16221896 | doi = 10.1093/molbev/msj030 | doi-access = free }} the R-package, phangorn,{{cite journal| vauthors = Schliep K, Potts AJ, Morrison DA, Grimm GW |title=Intertwining phylogenetic trees and networks|journal=Methods in Ecology and Evolution|volume=8|issue=10|year=2017|pages=1212–1220 |doi=10.1111/2041-210X.12760|doi-access=free}}{{cite web | vauthors = Schliep KP | date = 2018 | title = R package: Estimating phylogenetic trees with phangorn. | url = https://cran.r-project.org/web/packages/phangorn/vignettes/Trees.pdf }}

and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.{{cite journal | vauthors = Cardona G, Rosselló F, Valiente G | title = Extended Newick: it is time for a standard representation of phylogenetic networks | journal = BMC Bioinformatics | volume = 9 | pages = 532 | date = December 2008 | pmid = 19077301 | pmc = 2621367 | doi = 10.1186/1471-2105-9-532 | doi-access = free }}

Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, ancestral recombination graphs (ARGs) from binary sequences, median networks from a set of splits, optimal realizations and reticulograms from a distance matrix), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks).

Microevolution

Phylogenetic trees also have trouble depicting microevolutionary events, for example the geographical distribution of muskrat or fish populations of a given species among river networks, because there is no species boundary to prevent gene flow between populations. Therefore, a more general phylogenetic network better depicts these situations.{{cite journal | vauthors = Legendre P, Makarenkov V | title = Reconstruction of biogeographic and evolutionary networks using reticulograms | journal = Systematic Biology | volume = 51 | issue = 2 | pages = 199–216 | date = April 2002 | pmid = 12028728 | doi = 10.1080/10635150252899725 | doi-access = free }}

Rooted vs unrooted

;Unrooted phylogenetic network

:Let X be a set of taxa. An unrooted phylogenetic network N on X is any undirected graph whose leaves are bijectively labeled by the taxa in X.

A number of different types of unrooted phylogenetic networks are in use like split networks and quasi-median networks. In most cases, such networks only depict relations between taxa, without giving information about the evolutionary history. Although some methods produce unrooted networks that can be interpreted as undirected versions of rooted networks, which do represent a phylogeny.

;Rooted phylogenetic network

:Let X be a set of taxa. A rooted phylogenetic network N on X is a rooted directed acyclic graph where the set of leaves is bijectively labeled by the taxa in X.

Rooted phylogenetic networks, like rooted phylogenetic trees, give explicit representations of evolutionary history. This means that they visualize the order in which the species diverged (speciated), converged (hybridized), and transferred genetic material (horizontal gene transfer).

Classes of networks

{{missing information|section|what each of the three classes is; particularities of popular algorithms like neighbornet|date=November 2021}}

For computational purposes, studies often restrict their attention to classes of networks: subsets of all networks with certain properties. Although computational simplicity is the main goal, most of these classes have a biological justification as well. Some prominent classes currently used in the mathematical phylogenetics literature are tree-child networks,{{cite journal | vauthors = Cardona G, Rosselló F, Valiente G | title = Comparison of tree-child phylogenetic networks | journal = IEEE/ACM Transactions on Computational Biology and Bioinformatics | volume = 6 | issue = 4 | pages = 552–69 | date = October 2009 | pmid = 19875855 | doi = 10.1109/TCBB.2007.70270 | hdl = 2117/7146 | arxiv = 0708.3499 | s2cid = 405065 }} tree-based networks,{{cite journal | vauthors = Francis AR, Steel M | title = Which Phylogenetic Networks are Merely Trees with Additional Arcs? | journal = Systematic Biology | volume = 64 | issue = 5 | pages = 768–77 | date = September 2015 | pmid = 26070685 | pmc = 4538883 | doi = 10.1093/sysbio/syv037 }} and level-k networks{{Cite journal| vauthors = Choy C, Jansson J, Sadakane K, Sung WK |date=2005-05-20|title=Computing the maximum agreement of phylogenetic networks|journal=Theoretical Computer Science|series=Pattern Discovery in the Post Genome|volume=335|issue=1|pages=93–107|doi=10.1016/j.tcs.2004.12.012|issn=0304-3975|doi-access=free}}{{Cite web|url=http://phylnet.univ-mlv.fr/isiphync/index.php|title=ISIPhyNC - Information System on Inclusions of Phylogenetic Network Classes|website=phylnet.univ-mlv.fr|access-date=2019-06-13}}

Software to compute phylogenetic networks

[http://bioinfo.cs.rice.edu/PhyloNet PhyloNet], A Java-based software package that builds phylogenetic networks taking ILS, HGT etc. into consideration.
[http://crsl4.github.io/PhyloNetworks.jl/latest/ PhyloNetworks], a [https://julialang.org Julia] package for the manipulation, visualization, inference of phylogenetic networks, and their use for trait evolution.
[http://www.fluxus-engineering.com/sharenet.htm Network], Free Phylogenetic Network Software. Network generates evolutionary trees and networks from genetic, linguistic, and other data.
[http://evolution.genetics.washington.edu/phylip/software.html Phylogeny programs], some of which compute phylogenetic networks
[https://web.archive.org/web/20141125081801/http://www.lirmm.fr/~gambette/PhylogeneticNetworks/show.php?keyword=programs List of programs for phylogenetic network reconstruction, evaluation, visualization, etc.]
SplitsTree
Dendroscope
[http://www.trex.uqam.ca/index.php?action=hgt&project=trex Network inferring on the T-REX server]
[http://darwin.uvigo.es TCS], Phylogenetic networks from DNA sequences or nucleotide distances using statistical parsimony.
[http://darwin.uvigo.es NetTest], Characterization of phylogenetic networks.{{cite journal | vauthors = Arenas M, Patricio M, Posada D, Valiente G | title = Characterization of phylogenetic networks with NetTest | journal = BMC Bioinformatics | volume = 11 | pages = 268 | date = May 2010 | pmid = 20487540 | pmc = 2880032 | doi = 10.1186/1471-2105-11-268 | doi-access = free }}
[https://cran.r-project.org/web/packages/phangorn/index.html phangorn: Phylogenetic Reconstruction and Analysis]
[https://github.com/Stephane-S/Simplot_PlusPlus SimPlot++] Sequence similarity network analysis.{{cite journal |last1=Samson |first1=Stéphane |last2=Lord |first2=Étienne |last3=Makarenkov |first3=Vladimir |title=SimPlot++: a Python application for representing sequence similarity and detecting recombination |journal=Bioinformatics |date=26 May 2022 |volume=38 |issue=11 |pages=3118–3120 |doi=10.1093/bioinformatics/btac287|pmid=35451456 |arxiv=2112.09755 }}

phylogenetic network

Microevolution

Rooted vs unrooted

Classes of networks

Software to compute phylogenetic networks

References

Further reading